Insights into protein–ligand interactions: mechanisms, models, and methods

X Du, Y Li, YL Xia, SM Ai, J Liang, P Sang… - International journal of …, 2016 - mdpi.com
Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

Predicting protein–protein interactions from the molecular to the proteome level

O Keskin, N Tuncbag, A Gursoy - Chemical reviews, 2016 - ACS Publications
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …

PRODIGY: a web server for predicting the binding affinity of protein–protein complexes

LC Xue, JP Rodrigues, PL Kastritis, AM Bonvin… - …, 2016 - academic.oup.com
Gaining insights into the structural determinants of protein–protein interactions holds the key
for a deeper understanding of biological functions, diseases and development of …

Contacts-based prediction of binding affinity in protein–protein complexes

A Vangone, AMJJ Bonvin - elife, 2015 - elifesciences.org
Almost all critical functions in cells rely on specific protein–protein interactions.
Understanding these is therefore crucial in the investigation of biological systems. Despite …

Updates to the integrated protein–protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2

T Vreven, IH Moal, A Vangone, BG Pierce… - Journal of molecular …, 2015 - Elsevier
We present an updated and integrated version of our widely used protein–protein docking
and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality …

SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation

J Jankauskaitė, B Jiménez-García, J Dapkūnas… - …, 2019 - academic.oup.com
Motivation Understanding the relationship between the sequence, structure, binding energy,
binding kinetics and binding thermodynamics of protein–protein interactions is crucial to …

SAbDab: the structural antibody database

J Dunbar, K Krawczyk, J Leem, T Baker… - Nucleic acids …, 2014 - academic.oup.com
Structural antibody database (SAbDab; http://opig. stats. ox. ac. uk/webapps/sabdab) is an
online resource containing all the publicly available antibody structures annotated and …

Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation

K Van Roey, B Uyar, RJ Weatheritt, H Dinkel… - Chemical …, 2014 - ACS Publications
The eukaryotic cell is a bustling collection of macromolecules acting cooperatively to
mediate the functions required for cell viability. Specific, context-dependent and tightly …

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

PL Kastritis, AMJJ Bonvin - Journal of The Royal Society …, 2013 - royalsocietypublishing.org
Interactions between proteins are orchestrated in a precise and time-dependent manner,
underlying cellular function. The binding affinity, defined as the strength of these …

Techniques for the analysis of protein-protein interactions in vivo

S Xing, N Wallmeroth, KW Berendzen… - Plant physiology, 2016 - academic.oup.com
Identifying key players and their interactions is fundamental for understanding biochemical
mechanisms at the molecular level. The ever-increasing number of alternative ways to …